Freak spaghetti arrangement?

Synthetic Life.

Spontaneous living cells in a test tube from simple ingredients?
Well no …..not quite…. we supply the carefully made membranes….oh and the 36 enzymes…. Oh and also the ribosomes…..oh and also the genetic information! But we are nearly there!

At least this is the illusion that some origin of life researchers seek to indicate.

Dr. Giovanni Murtas from the Synthetic Biology and Supramolecular Chemistry group at RomaTre University says:

"We can prove at this point that we can have protein synthesis with a minimum set of enzymes - 36 at the moment."

The fluescent green colouring indicates that these "primitive cells" can synthesize a protein from the supplied genetic information.

According to the guardian account this result “will teach us about the earliest stirrings of life in Earth’s primeval slime some 3.5bn years ago.”

Yerrr sure!

I would have thought that to any unbiased observer this result simply reminds us all that there is no hope that the primeval slime…no matter how exotic and how many billion years you give it will ever produce a living organism with minimal information and functioning protein machinery.

The information to specify such elegant structures as these does not hang around in primeval slime waiting for 36 enzymes and a few ribosomes to arrive.


I am not against this kind of work at all... I applaud it! What I am against is giving the impression that the solution to the problem of the origin of life is nearly solved and it is just a matter of time before we crack it.

Melanie Phillips - Life in a random Universe?

"Moreover, since science essentially takes us wherever the evidence leads, the findings of more than 50 years of DNA research — which have revealed the almost unbelievable complexity of the arrangements which are needed to produce life — have thrown into doubt the theory that life emerged spontaneously in a random universe."

See the whole piece here.

Science Vs Religion.

Publication of Steve Fuller’s Dissent over Descent has been delayed until Spring 2008. However, in the meanwhile, he has just published another book relating to ID, Science vs Religion? Intelligent Design and the Problem of Evolution (Polity). You can peek inside the book by going to the Amazon website.

Fuller will be speaking at the Leeds University conference, ‘Darwinism after Darwin’, on 3-5 September. This includes an appearance on a panel discussing Richard Weikart’s controversial From Darwin to Hitler (Palgrave), with Weikart as respondent. For more information about this conference, which is open to the public, see the website: http://www.darwinismafterdarwin.com/

Darwin or Design.

Jason Rennie, the young Australian producer of the on-line ‘thesciphishow’, has released ‘Darwin or Design’, 9.5 hours of interviews with various people on either side of this controversy.

The links to these interviews are here.


An overview of Evolution
Chapter 1 : PZ Myers, An overview of Evolution and ID 15:48
Chapter 2 : Sean Carroll, What is Evo Devo ? 20:17
Chapter 3 : Nick Matzke, Can the Flagella Evolve ? 29:27

Design in the ID advocates own words
Chapter 4 : Salvador Cordova, What is ID ? 20:20
Chapter 5 : Mike Behe, What is Irreducible Complexity ? 17:51
Chapter 6 : Angus Menuge, Agency and how to identify it 18:28
Chapter 7 : Guillermo Gonzalez, The Privileged Planet 17:26
Chapter 8 : Joey Campana, Does ID research actually exist ? 26:17
Chapter 9 : James Shapiro, Sentient Cells ? 33:50
Chapter 10 : Mike Gene, What is Front Loading ? 23:37

ID's critics
Chapter 11 : Elliot Sober, ID and the Philosophy of Science 10:46
Chapter 12 : Scott Turner, The problem of Design 24:02
Chapter 13 : Glenn Morton, Can ID work in Biology ? 15:19
Chapter 14 : Ryan Nichols, Are ID and Theology Inseperable ? 14:28
Chapter 15 : Georgia Purdon, Isn't ID just Creationism in Disguise ? 21:44

ID, The Philosophy of Science, History and The Law
Chapter 16 : David Livingstone, Evolution and Christianity, The History 32:37
Chapter 17 : Del Ratzsch, Can ID be Science ? 25:38
Chapter 18 : Massimo Pigliucci, Evolutionary Epistemology and ID 28:34
Chapter 19 : Henry Schaefer, Science and Religion 14:40
Chapter 20 : Donald McConnell, Intelligent Design, Creationism and The Law 34:42
Chapter 21 : Steve Fuller, ID & Social Epistemology 19:11

ID in the Wild
Chapter 22 : John Davison, The Price of Dissent 35:26
Chapter 23 : Denyse O'Leary, ID & The Media 22:51
Chapter 24 : Geoff Simmons, Darwinism, ID & Medicine 27:40
Chapter 25 : Rob Sawyer, Calculating God 25:27

Expelled!

A trailer for this film due to be released on Darwins birthday (February 12th next year) is now available here.

Press release is here.

It looks interesting!

Separation of Science and Religion

The separation of the religious and the scientific means in the end the separation of the religious and the true; and this means that religion dies among true men.

(James Denney - Studies in Theology 1894)

Teaching Intelligent Design is the perfect recipe for mass producing suicide bombers!

This is apparently what Harry Kroto (an otherwise intelligent fellow) seriously believes!

The Education Guardian included this extract from Sir Harry Kroto’s (Francis Eppes professor in the department of chemistry and biochemistry at Florida State University) “Can the Prizes Still Glitter? The Future of British Universities in a Changing World” published by Agora.

Do I think there is any hope for UK? I am really not sure. It is beyond belief that in the 21st century, our prime minister and the Department for Education and Skills are diverting taxpayers' money to faith-based groups intent on propagating culturally divisive dogma that is antagonistic to the secular, enlightened philosophy that created the modern world.

It is a scandal that the present system is enabling a car salesman to divert significant government funds to propagate dogma such as "intelligent design" in our schools. State funds are also being used to support some schools that abuse impressionable young people by brainwashing them into believing that non-believers will burn for all eternity in the fires of hell. This policy is a perfect recipe for the creation of the next generation of homegrown and state-educated suicide bombers.

I think there is every likelihood that the lack of scientifically educated and aware young people in the UK will result in ever poorer performance on a global scale, and a takeover by the next generation of young Chinese and Indians, ravenous for the scientific knowledge that will free them from the shackles of present poverty levels. They are being actively encouraged by their governments, who understand that the future lies in a scientific education based on doubt and questioning, rather than on belief.

It is truly disturbing that a well-funded cohort of religious groups - aided, abetted and condoned by the Labour government - is undermining our science education. If they achieve any more success in their subversion of the intrinsic secular safeguards embodied in our democratic institutions and our educational system, there can be no doubt there is major trouble ahead. So my final message is: "Do Panic!"

Harry Kroto is a brilliant scientist. However as an example of what he describes as “the enquiring mindset” he leaves a great deal to be desired with regards to the influence of his own materialist mindset on his convictions about those who disagree with his philosophy.

It is scarcely credible that a well educated scientist feels that he can write such patently ridiculous, offensive, ill informed, vitriolic gibberish.

If he feels as strongly about this as he appears to from this extract then at the very least he ought to get his facts straight! Being passionate about something is one thing. Being passionate about and publishing your passionate rhetoric without checking your facts is the quickest way to make yourself and your cause appear ridiculous.

1. What evidence is there that a traditional Christian education produces a higher proportion of suicide bombers than an atheistic, materialistic, relativistic one or any other sort of education? Presumably Kroto lumps all religious education together as being equally destructive. If you are religious then you are a secret member of the Taleban. So much for a carefully nuanced and a meticulously researched piece of prose!
2. What evidence does he have that a particular car salesman is in favour of teaching any intelligent design or creationism in science lessons let alone that he is diverting government funds for this purpose?
3. What right has he got to claim all the improvements in the modern world as the natural children of “secular, enlightened philosophy” (which presumably means materialism)?
4. What evidence does he have that there is “brainwashing” taking place in any UK state school?
5. Since when did the UK become a secular materialist state?

I share Prof Kroto’s concern for improved science education at the university level in the UK. However I do not think that insisting upon an ideological commitment to materialism like the bad old days of the USSR is the way to catch up with the US where there is considerably more creationism and intelligent design than in the UK.

Evolution becomes fact.

"For many years it was possible to doubt the validity of Darwin's theory, but skepticism is not a tenable position today."

Cynthia Russett, Darwin in America 1976, p210

When did this transition take place? What were the key discoveries that resulted in this transition?

Science and Materialism.

I was interested in this quote from Martin Redfern's article.

"Everyone is entitled to their beliefs, but what annoys Eugenie Scott is the way in which the received wisdom of Genesis is given equal or higher status to scientific evidence; and the way in which the latter is used selectively.

'In the card game of creationism, the Bible trumps science every time,' she says.

But in her game, science is dealt a hand that is purely materialistic. Ideas of a supernatural being belong in a different game, be it philosophy or theology."

Fuller Dissent.

Steve Fuller has a new book out:

I have pre-ordered a copy so I will be interested in his view of this controversy on this broad canvas. I wonder if his arguments will include things like this?

Methodological Naturalism

Just over a year ago Paul Nelson posed this question here

"Ask oneself a simple question. Suppose life actually were designed by a nonhuman intelligence -- would methodological naturalism allow us to discover that? If the answer is no, then methodological naturalism hinders scientific discovery and dictates the shape of reality as thoroughly as philosophical naturalism. If the answer is yes, then methodological naturalism is superfluous and says nothing more than that science should be empirical and testable."


Do you agree?

Questions....

1. Is Methodological naturalism (MN) an essential commitment for scientific progress?
2. Is MN falsifiable? Could MN be false? How would we know?
3. Is the origin of life without intelligence reasonable without a prior commitment to MN? Is it acceptable scientifically to think that the origin of life requires an intelligent agent?
4. Is MN significantly different from philosophical naturalism? Are MN and consistent Theism compatible?

Douglas Axe - J.Mol.Biol.(2000) 301, 585-595

Thanks to "Smokey" for the paper.
Previous blog post here.
This paper examines the idea that there are many amino acid residues in an enzyme which almost act as non-specific spacer residues and the nature of their side groups is almost completely irrelevant to the enzyme function. The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous. Axe’s arguments rely on data from two different, unrelated enzymes.

Firstly, several amino acids are exchanged with several other very similar amino acids on the surface of the molecule and away from the active site and the effects measured. When roughly 1 in 5 of these residues is changed this results in complete loss of function in both enzymes examined.

Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive.

Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features.

These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues.

It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues.

Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous.

Away for a few days.

I will not be around for a few days so I will look at comments when I get back.

Inside the Cell.

David Goodsell is a biochemist who is also an excellent artist. He has combined these skills in the production of beautiful paintings which seek to portray an idea of the molecular biology of the cell. More of his illustrations are here. He kindly gave me permission to use these pictures here:

This picture shows part of a bacterium.

(Can you spot the motor? :-) )

This one shows a section across a red blood cell with the blood serum outside the cell.

This is an enlargement of a small part of the same picture.

This picture shows an HIV virus particle under attack from the immune system.

(Thanks to Tony Jackson for the original link.)

"Strong indications of design."

Nick Jackson of the Independent interviews Stuart Burgess who argues that there are "strong indications of design" in the four bar linkage of the knee joint. The report is here.

The making of "The Root of All Evil."

In response to this question:
Why have you not engaged in public debate with Alister McGrath, Mary Midgley, Michael Ruse, Keith Ward, or indeed anyone else who would present you with a serious challenge? JAMES RADFORD, By e-mail
Richard Dawkins replied:
The producers of my Channel 4 documentary [Root of All Evil?] invited the Archbishop of Canterbury, the Cardinal Archbishop of Westminster and the Chief Rabbi to be interviewed by me. All declined, doubtless for good reasons. I don't enjoy the debate format, but I once had a public debate with the then Archbishop of York, and The Observer quoted the verdict of one disconsolate clergyman as he left the hall: "That was easy to sum up - Lions 10, Christians nil."
(from here)


Alistair McGrath gives a somewhat different slant...
Dawkins and I both love the sciences; we both believe in evidence-based reasoning. So how do we make sense of our different ways of looking at the world? That is one of the issues about which I have often wished we might have a proper discussion. Our paths do cross on the television networks and we even managed to spar briefly across a BBC sofa a few months back. We were also filmed having a debate for Dawkins's recent Channel 4 programme, The Root Of All Evil? Dawkins outlined his main criticisms of God, and I offered answers to what were clearly exaggerations and misunderstandings. It was hardly rocket science.
For instance, Dawkins often compares belief in God to an infantile belief in Santa Claus or the Tooth Fairy, saying it is something we should all outgrow. But the analogy is flawed. How many people do you know who started to believe in Santa Claus in adulthood?
Many people discover God decades after they have ceased believing in the Tooth Fairy. Dawkins, of course, would just respond that people such as this are senile or mad, but that is not logical argument. Dawkins can no more 'prove' the non-existence of God than anyone else can prove He does exist.
Most of us are aware that we hold many beliefs we cannot prove to be true. It reminds us that we need to treat those who disagree with us with intellectual respect, rather than dismissing them - as Dawkins does - as liars, knaves and charlatans. But when I debated these points with him, Dawkins seemed uncomfortable. I was not surprised to be told that my contribution was to be cut. The Root Of All Evil? was subsequently panned for its blatant unfairness. Where, the critics asked, was a responsible, informed Christian response to Dawkins? The answer: on the cutting-room floor.
(from here)

Comments.

The comments section at IDintheUK has been entirely uncensored up till now (apart from really foul comments and obvious advertising.) I would like it to remain like this. I have learned a lot from the very high quality of comments from people on both sides of this argument. This seems to me a great benefit of this kind of site.

In order for this to continue it does require some self discipline on the part of the commenters.

Generally you have responded well to previous pleas.

I would like people to feel free to comment under whatever name they like and to be able to comment annonymously if they so choose. I think that part of good blog behaviour is to respect that choice. Attacks on another commenter because of their background and percieved or actual bias are to be avoided- it is the arguments about the data and its interpretation that we should focus on.

Please try to avoid overly emotive language- I know that many commenters feel very very strongly about this area - It is good to feel strongly about truth and to expose what is not true ruthlessly and energetically. However resorting to the red card "LIAR" is rarely helpful in my experience. Even if you are convinced that someone is deliberately and knowingly lying it is better to suggest that they may be mistaken first and point to the evidence. If you must make an allegation of deliberate, knowing deception please make sure you have a cast iron case and please try to do it as little as you possibly can.

The Dawkins Delusion.

I have noticed several pieces about this odd phenomenon. Bill Dembski seems to have got hold of a very strange interview with Dr Terry Tommyrot, available here. Another interesting report of a discussion on the same subject is here.

Possible Pathways for the evolution of intracellular transport.

In his book “Darwin’s Black Box Behe made the claim with regards to the cellular transport systems that:
"A search of the professional literature and textbooks shows that no one has ever proposed a detailed route by which such a system could have come to be."

Some commenters here have argued that Behe is being intentionally deceptive they argue that there is an abundance of published material – shelf loads of it - that give a clear outline of how a pathway transporting a newly synthesized protein to an intracellular compartment could arise.

Some suggestions were given as to where I should start – (I acknowledge that they were probably hurriedly put together sources by scientists who are very busy doing more important work than arguing with me and I do appreciate the attempt to provide me with the references.)

http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html

This is sequence comparisons in the myosin superfamily looking at homologies between the different types of myosin molecules in different organisms.

http://www.pnas.org/cgi/content/full/103/10/3498
This is the attempted production of a phylogenetic tree comparing different types of myosin molecule.

The Richards and Cavalier Smith Nature paper is similar and suggests that the most primitive eukaryotes had three types of myosin from which all eukaryotic myosins come but that does not really help me.

This gives 111 delightful titles but not really what I am after. They are mainly phylogenetic trees and studies of sequence similarities. Behe accepts that there are an abundance of this kind of study.

What I am after is a simple step by step process whereby a single transport system from protein translation completion to function in a separate compartment can arise. It does not have to be a DVD of the process happening just a suggestion of some of the useful steps along the way.
I am thinking of the kind of thing that Matt Inlay produced in response to Behe’s Immunology chapter (here) or Nick Matzke’s response to the flagellum chapter ( here)


Tony’s scenario:
This problem concerns the way proteins are targeted to the mitochondria. These organelles (again, they’re shown in your diagram) are responsible for supplying a major fraction of the cell’s energy needs. They are distantly descended from free-living bacteria that began a symbiotic relationship with an early eukaryote. As part of that evolutionary history, mitochondria still retain a small genome which encodes a few of the proteins required by the organelle. However, over evolutionary time there has been a general drift towards more and more mitochondrial genes being transplanted to the nucleus. Mitochondrial proteins produced from such nuclear genes somehow have to get to their correct organelle. How do they do that? It turns out that such proteins contain, right at the start of their amino acid sequence, a so called ‘targeting signal’ made of about the first ten or so amino acids and which docks with import machinery in the mitochondrion. A mitochondrial gene newly transplanted into the nuclear genome must acquire this signal or it risks turning into a pseudogene. So how easy is it to acquire a functioning targeting signal? Some years ago a clever experiment was performed to find out. It’s a neat example of how our intuitive ‘gut feelings’ about these issues can lead us badly off-course. The scientists took a gene for a mitochondrial protein, then replaced its normal targeting signal with random DNA sequences sized to encode between about ten and thirty amino acids. They then determined what fraction of these random sequences acted as functioning mitochondrial targeting signals for the protein.What do you think the answer was? One in ten million? Or some other Dembski number perhaps? Actually, they got a remarkable 3 to 5%! Subsequent work with more truly random and uniformly-length sequences increased this estimate still further. Evidently, it’s almost ridiculously easy to evolve working targeting signals. One more point is worth making here. Because the results were so striking and the way the experiment was conducted was so elegant, this work is rather well known in the field. It was published in 1987 – almost ten years before Behe wrote his book. Yet he tells us with a straight face that no experiments have been done to address the evolutionary origins of protein traffic!


Tony’s point here is that the ID code for the mitondrial car park is pretty easy to forge. The fellow checking the ID’s is a pretty sloppy fellow and a great variety of ID sequences will do.

However let us imagine that this putative mitochondrial gene is the very first one to complete the journey into the cell’s genome. Let us also assume that the appropriate insertion of DNA occurs of the correct length and with the approximately correct sequence. Is this all that is required for the newly made protein to find its way into the mitochondrion? Is it just a single rough ID sequence that is needed or are other modifications required in the mitochondrial genome and elsewhere in the cell?

Molecular Meccano

Described by some researchers as a strange form of molecular “lego” and by others as “molecular basket weaving” the beautifully shaped propeller like molecules of clathrin have a crucial role in the cell’s internal distribution network. Another description in the literature is “groovy” which I think is about right! A single clathrin complex is made up of 3 light chains together with 3 heavy chains

to form the propeller like structure called a “triskelion” meaning three-legged.
These 3 legged units can be attracted to a membrane by a variety of different molecular structures on the surface of the membrane. As they are attracted they begin to associate

and as they associate they begin to bend the membrane inwards. The structure grows to form a complete and beautiful basket or cage around a little blister of membrane which is eventually pinched off to form a separate bubble inside the membrane.

At this point the clathrin complexes can be removed and reused elsewhere.

The diagram below is adapted from here (thanks to Dr. Tony Jackson)

A Quicktime Movie is here showing the assembly of a clathrin coated vesicle. (You may have to wait a little time for it to load.)

A Flash animation of the budding off of a clathrin vesicle is available here.

Intracellular Transport systems

There are two types of living cells that we know of on earth-
1. Prokaryotic cells:

2. Eukaryotic cells [from the greek word karyon meaning nut or kernel – prokaryotic meaning “before a kernel” and eukaryotic meaning “with a true kernel” – the kernel being the nucleus of the cell.]

Eukaryotic cells not only have a “kernel” the nucleus but they have a goodly number of other internal compartments inside the cell too.

There is the complex structure of the onion like “endoplasmic reticulum” around the nucleus, there is the “golgi apparatus” looking like a pile of plates ready for a feast, there are the mitochondia looking like sausages out of some crazy sausage machineand there are the lysozymes- the waste recycling plants of the cell.

These different compartments each have their special function inside the eukaryotic cell.

The problems of transport are therefore much more complicated in the eukaryotic cell than they are in the prokaryotic cell.

It is these traffic problems that Behe mentions in chapter 5 – (From here to there) of “Darwin’s black box”

He first uses two analogies to explain the problem he is seeking to elucidate.

1. The delivery of urgently needed vaccine to an area of the country where there is an outbreak of a highly infectious viral disease. If the correct vaccine arrives at the correct location then lives can be saved- if not lives will be lost. Behe then imagines a film director making a film called “epidemic” in which the vaccine labels get muddled – This situation is similar to the situation inside a cell he argues when the transport system breaks down- death is the result.
2. He then imagines a robotic space ship exploring space with its battery crusher compartment, its library, its master machines and so on- This imaginary space probe is then compared to a cell

He then asks…. Is this analogy real?

This is illustrated using a protein he calls “garbigase.” A temporary copy of the relevant section of data from the DNA library is made- the messenger molecule. This messenger molecule passes to a nuclear pore- a tiny little door in the wall of the kernel. Proteins in the pore recognise the molecule in a process analogous to a challenge of identity with a secret password being given and the pore opens. In the cytoplasm a master machine the “ribosome” begin the process of converting the linear coded data into a 3D machine- in a process which biochemists have aptly named “translation” to make part of a brand new gleaming machine.

Diagram of translation:

Diagrams of a ribosome:

The first part of the machine to be made is a special combination code which quickly and neatly sticks to a code “hood” (signal recognition particle) causing the translation process to pause. The hooded new machine then locates a docking site in the surface of the onion. The docking process un-pauses the translation process and the newly made full length machine – a baby garbigase molecule - is fed into the inside of the onion compartment. As it passes into this new compartment the special code sequence to gain its safe entry is clipped off and a large carbohydrate molecule is bolted onto it.

Special proteins then cause a bubble of the onion wall to form and this pinches off into a separate little bubble containing molecules of the new garbagase protein. This little package then moves to another compartment called the Golgi apparatus and joins with the wall of this new compartment.

This kind of process happens two more times as the enzyme passes through several compartments of the Golgi apparatus. Another carbohydrate group is added to the enzyme and this is then trimmed by another enzyme leaving an special code MI-6 molecule.

In the final compartment of the golgi apparatus 3 blade propellor proteins snap together in a patch forming a bubble making cage. Within this bubble there is a MI-6 checker protein that binds to MI-6 pulling it into the bubble before it buds off. On the outside of the bubble is a tiny rabbit-SNARE protein that binds only to a tiny rabbit- proteins on the surface of the final compartment to which this little bubble is journeying.

Once the final docking process has completed further special membrane fusing proteins join the bubble to the wall of the waste disposal compartment so that it becomes part of it emptying its contents into its final destination.

A very controversial paper!

Doug Axes’ work was controversial even as he was carrying it out. It was funded by an Institute that never under any circumstances funds anything but misguided PR material- The Discovery Institute. When another researcher in his lab pointed to the Discovery Institute's agenda and suggested that Axe be asked to leave, Prof Fersht refused. (New Scientist article)

It was controversial when it had been published with Dembski hailing it as a peer reviewed publication which supported his arguments.

Axes’ work has continued to be controversial with the set up of the Biologic Institute and his announcement that he does consider his work as supportive of the ID view.

Ed Brayton (here and here) thinks that the Journal of Molecular Biology accepted a paper in which the author got the title of his paper to mean the opposite of what his results suggested!

“The 2000 JMB paper did not show "severe sequence constraints" at all. It showed quite the opposite, that you could make massive changes in the sequence of amino acids in an enzyme, knocking out 10, 20, even 30 amino acids at a time, without completely destroying the function of the enzyme. It showed that you could make 10 substitutions at a time with only a negligible effect on the enzyme's function. And this is "severe sequence constraints"? Not even close.”

The title according to Ed should not have been “Extreme functional sensitivity to….” But Extreme functional INsensitivity to…” I immediately thought that the fact that the paper’s author and the papers reviewers made such a monumental error and that Ed managed to come to the rescue and point this out was rather odd to say the least. That it managed to get through the JMB peer review process without anyone noticing that the title was saying the opposite of the results seems quite remarkable to say the least! Perhaps it was a simple printing error?

Matt Inlay critiques the early claims that Dembski made for this research. Interestingly Matt Inlay does not mention that Axe got his title wrong.

Arthur Hunt likewise does not mention that Axe got his title so completely wrong and argues that of all the values for enzyme functionality in possible sequence space the lower ones give easily attainable rates in bacterial populations. However the much smaller populations in larger animals still present difficulties for explaining the origin of their unique proteins.
(Interestingly Arthur Hunt mentions that Douglas axe helped him with early drafts of this essay.)

Hunt present the enzyme activity as hills with a wide or narrow base. The size of the base of the hill indicates the likelihood of finding a functional protein by random mutation.

Personally I like my golf course analogy better which turns the diagram upside down. (here and here)

Abstracts of Axes Papers: here and here

Heaven and Earth

ID was one of the subjects under discussion on the Heaven and Earth programme.
Prof. Mark Walport (Director of the Wellcome Trust) spoke against ID maintaining that:

"Evolution is truth now... there is huge anounts of experiment evidence to back it up."

Dr Alistair Noble spoke in defence of ID:

"Intelligent design is a very ancient idea going back at least to the Greeks - It maintains that there is evidence for design in the universe. The constants of physics are finely tuned for life and this looks like design, complex systems are necessary for life and these look designed above all the coded information locked into DNA looks designed."

Former Education Secretary David Blunkett "helpfully" added that ID is “just a much more sophisticated version of creationism.”

Simon Barrow, of "Ekklesia" dismissed ID as a “mistaken religious ideas” and “a political and religious problem”.

Dr Noble responded by distingishing ID from creationism in the following way:

“the difference between intelligent design and creationism is that they have very difference starting points. I would want to insist that the starting point for intelligent design is scientific observation.”

Intelligent Design and Evolution have the same status as scientific theories.

Royal Holoway University of London are hosting a debate on the above proposition on 21st February at 5.00pm.
Steve Fuller graduated as a sociologist and then studied the history and philosophy of science and has focused on the writings of Thomas Kuhn and Karl Popper. He describes himself as a secular humanist.

He has commented on the Dover judgement (in which he was a witness) here.
He has explained how he became involved in the ID debate here.
A brief outline of a previous debate with Jack Cohen is here.

Lewis Wolpert is a developmental biologist who was made a Fellow of the Royal Society in 1980 and was awarded the CBE in 1990. He was for 4 years Chairperson of the Committee for Public Understanding of Science. He is a well known rationalist.

Given that we have a rationalist debating a secular humanist this hardly looks like a standard religion versus science debate!

Abiogenesis and the 2nd Law of Thermodynamics.

Previous related posts:
Andy MacIntosh and the 2nd Law.
The idea of unintelligent Abiogenesis.
Is Abiogenesis Falsifiable?

This post is based on Walter Bradley’s chapter on “Information, Entropy and the Origin of Life.” In “Debating Design” Edited by Ruse and Dembski and published by Cambridge University Press.

Walter L. Bradley was one of the authors of “The Mystery of Life’s Origin.” which remains as the best selling advanced level text on the Origin of Life.

Bradley states that the second law of thermodynamics (2lot) and the theory of evolution are two of the three major scientific discoveries of the nineteenth century with Maxwell’s field equations for electricity and magnetism being the third. He is intrigued that the theory of evolution and the 2lot appear to be in conflict. The 2lot suggests a progression to disorder from order, from complexity to simplicity. Evolution involves progression to increasingly more complex forms of living organisms.

Erwin Schroedinger noted that living systems are characterized by highly ordered, aperiodic structures that survive by drawing “negentropy” from their environment and feeding on it! Today we recognise Schroedinger’s ordered structures as the complex biopolymers of protein and nucleic acids.

Living organisms use information stored in these biopolymers to resist the pull of the 2lot towards equilibrium. They are able to store information, to replicate with minimal information loss and they are able to feed on “negentropy.”

The existence of these three abilities allow us to understand how living organisms can continue to exist without violating the 2lot but the difficulty is understanding how these three abilities came to exist without violating the 2lot. This is the greatest mystery in science. At the heart of this problem is the difficulty of explaining how the complex specified information within these biopolymers can originate.

Bradley discusses the significant quantities of Shannon information that are stored in cytochrome c and in the E.coli bacterial chromosome.

At best the 2lot gives a very small yield of unsequenced polymers that have no biological function. The sequencing required for function is not facilitated by the 2lot.

Bradley then goes on to discuss the various origin of life scenarios that have been proposed in the light of the problem of the need for information and the pressure of the 2lot towards disorder.

He concludes: The origin of life seems to be the ultimate example of irreducible complexity. I believe that cosmology and the origin of life provide the most compelling examples of Intelligent design in nature. I am compelled to agree with the eloquent affirmation of design by Harold Morowitz (1987):

“I find it hard not to see design in a universe that works so well. Each new scientific discovery seems to reinforce that vision of design. As I like to say to my friends, the universe works much better than we have any right to expect.”

The 2nd Law of Thermodymamics and Abiogenesis.

I commented on William Crawley’s “Sunday Sequence” and its aftermath here.

William Crawley has put several posts up following this. “Finding Darwin’s God” a piece on Ken Miller. Richard Dawkin’s letter to the Guardian. A piece on Andy Macintosh. A piece on the letters defending Andy Macintosh. Andy Macintoshes reply. Since then William Crawley has chosen Richard Dawkins as his Blog’s Person of the year. He has linked to a Salon interview with Ron Number’s the author of “The Creationists” and blogged on the letter from senior academics defending TiS.

Clearly William Crawley has a more than passing interest in the brewing "Biological Origins War" in the UK.

I was very interested in the exchange between Richard Dawkins (RD) and Andy MacIntosh (AM) and its aftermath. RD clearly thought that he was on to a big hitting winner with AM mentioning that the 2^nd Law of thermodynamics rules out an unintelligent origin for biological information systems. RD seemed to be keen that Leed’s University should take action against one of its professors speaking in this way about a subject that is clearly within his own area of special competence- thermodynamics.

I got the impression RD really wanted AM to say something like “The 2^nd law of Thermodynamics means that evolution is impossible.” RD could then show watertight evidence for micro-evolution and initiate a national UK science day of laughter at the silly creationists. However this is not what AM actually said. He has further clarified his position with a comment which has been published on William Crawley’s blog.

This is what he said:

Now that the 2nd law has had time to work on the Turkey this Christmas . . . maybe a few words are in order on thermodynamics and living machinery which I spoke about on the Sunday Sequence program on Dec 10th. I don't usually enter lots of blog discussions, but I see that you are having quite a debate here, so perhaps a word is in order from me. I do not on principle enter into any ad hominem attacks or respond to such against me. They do not add weight to any arguments and it is the science which is important.

The reason of course why this subject of origins will not go away is that there is a scientific case, whether Dawkins likes it or not, which is a challenge to the neo-Darwinian attempts to explain life in terms of common descent. It is a straightforward case of testable science versus the modern evolutionary ‘just-so’ story telling. Scientists like myself who believe in Creation have no problem with natural selection. It is simply the natural equivalent of artificial selection. But natural selection has no power to create new functional structures. It does not increase information and does not build machines which are not there already (either fully developed or in embryonic form).

The principles of thermodynamics even in open systems do not allow a new function using raised free energy levels to be achieved without new machinery. And new machines are not made by simply adding energy to existing machines. This was the point at issue in the programme of Dec 10th. Intelligence is needed.

And this thesis is falsifiable. If anyone was to take an existing chemical machine and produce a different chemical machine which was not there before (either as a sub part or latently coded for in the DNA template) then this argument would have been falsified. No one has ever achieved this.

I suggest that all the listeners read again if they have not done already, the excellent book by Wilder Smith called 'The natural sciences know nothing of evolution'. It is available on Amazon.

Clearly this kind of argument has been bubbling around for some time since Wilder Smith raised it. I do not think that when scientists of the standing of AM and Granville Sewel (University of Texas El Paso) are willing to stick their necks out over this that it can simply be dismissed as "showmanship bluffing" to a willing audience.

It is a also a subject which has also been raised by Walter Bradley (2004) "Information, Entropy, and the Origin of Life" pp 331-251 in Dembski and Ruse (eds) "Debating Design" Cambridge University Press.

I became interested in the concept of entropy in my A-level Chemistry classes but I really have only a very basic understanding of the concept. It seemed to me however that the 2^nd Law of Thermodynamics ruled out the idea that matter is eternal.

Those who believe that life originates without intelligence argue that all that is needed to produce life is energy plus matter plus lots of time. They tend to argue that the demonstration that this is true is the fact that life is here on earth!

AM, Wilder Smith, Walter Bradley,Granville Sewell and others clearly have the conviction that this formula is flawed and something else is needed.

Energy + Matter + Time + ? = Life (with its computer like information system)

The needed ingredient they say is a plan, an idea…intelligent design.

Prominent Academics support Truth in Science.

Previous posts on "Truth in Science":
http://idintheuk.blogspot.com/2006/09/launch-of-truth-in-science.html
http://idintheuk.blogspot.com/2006/11/truth-in-science-materials.html
http://idintheuk.blogspot.com/2006/10/truth-in-science.html

It has emerged that 12 prominent academics wrote to Tony Blair and Alan Johnson, the education secretary, last month arguing that ID should be taught as part of science on the national curriculum.

They included 1. Norman Nevin OBE, Professor Emeritus of Medical Genetics, Queen's University of Belfast, 2. Antony Flew, formerly professor of philosophy at Reading University; 3. Terry Hamblin, professor of immunohaemotology at Southampton University; 4. John Walton, professor of chemistry at St Andrews University, 5. David Back, Professor of Pharmacology at the University of Liverpool; 6. Steve Fuller, Professor of Sociology at Warwick University; 7. Mart de Groot, Director, Retired, Armagh Astronomical Observatory; and 8. Colin Reeves, Professor of Operational Research at Coventry University

http://www.timesonline.co.uk/article/0,,2087-2524442_1,00.html

http://www.truthinscience.org.uk/site/content/view/217/63